The development of a multiplex PCR assay for the detection of Fusarium oxysporum f. sp. cubense lineage VI strains in East and Central Africa

Ndayihanzamaso, Privat; Karangwa, Patrick; Mostert, Diane; Mahuku, George; Blomme, Guy; Beed, Fento; Swennen, Rony; Viljoen, Altus

doi:10.1007/s10658-020-02092-9

Cited by 19 publications

(10 citation statements)

References 47 publications

(69 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Presence/absence of SIX genes in the Colombian Foc TR4 genomes During the last ten years, several studies have developed molecular markers for detection of Foc TR4 (Matthews et al 2020;Magdama et al 2019;Ndayihanzamaso et al 2020;Dita et al 2010;Aguayo et al 2017;Lin et al 2013;Li et al 2013;Carvalhais et al 2019). This raises an important question: Are the existing molecular markers present in the Colombian Foc TR4 genomes?…”

Section: Genome Sequencing Of Colombian Foc Tr4 Isolatesmentioning

confidence: 99%

Genome Sequence Data Reveal at Least Two Distinct Incursions of the Tropical Race 4 Variant of Fusarium Wilt into South America

et al. 2023

View full text Add to dashboard Cite

The global banana industry is threatened by one of the most devastating diseases: Fusarium wilt (FWB). FWB is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), which almost annihilated the banana production in the late 1950s. A new strain of Foc, known as tropical race 4 (TR4), attacks a wide range of banana varieties including Cavendish clones which are the source of 99% of banana exports. In 2019, Foc TR4 was reported in Colombia, and more recently (2021) in Peru. In this study, we sequenced three fungal isolates identified as Foc TR4 from La Guajira (Colombia) and compared them against 19 whole-genome sequences of Foc TR4 publicly available, including four genome sequences recently released from Peru. To understand the genetic relatedness of the Colombian Foc TR4 isolates and those from Peru, we conducted a phylogenetic analysis based on a genome-wide set of single nucleotide polymorphisms (SNPs). Additionally, we compared the genomes of the 22 available Foc TR4 isolates looking for the presence-absence of gene polymorphisms and genomic regions. Our results reveal that (i) the Colombian and Peruvian isolates are genetically distant, which could be better explained by independent incursions of the pathogen to the continent, and (ii) there is a high correspondence between the genetic relatedness and geographic origin of Foc TR4. The profile of present/absent genes and the distribution of missing genomic regions showed a high correspondence to the clades recovered in the phylogenetic analysis, supporting the results obtained by SNP-based phylogeny.

show abstract

Section: Genome Sequencing Of Colombian Foc Tr4 Isolatesmentioning

confidence: 99%

Genome Sequence Data Reveal at Least Two Distinct Incursions of the Tropical Race 4 Variant of Fusarium Wilt into South America

et al. 2023

View full text Add to dashboard Cite

show abstract

“…If negative, the DNA was PCR amplified with Foc Clade A-specific primers (Mostert, unpublished data) to determine if the isolates belong to VCGs 0120/15, 0121, 0122, 0126, 0129/11, 01210 and 01219 [43]. If again negative, primers specific to Foc Lineage VI was used for PCR amplification, as described by Ndayihanzamaso et al [44] and Matthews et al [42]. Isolates that were negative for all three PCR amplifications were subjected to PCR assays specific to Foc Lineage VII, VCG 01218 and VCG 01221 (Mostert, unpublished data).…”

Section: Survey: Sample Processing and Detection Of Focmentioning

confidence: 99%

Geographical Distribution and Genetic Diversity of the Banana Fusarium Wilt Fungus in Laos and Vietnam

Chittarath

Nguyen²,

Bailey

et al. 2022

JoF

View full text Add to dashboard Cite

Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. cubense (Foc), poses a major threat to global banana production. The tropical race 4 (TR4) variant of Foc is a highly virulent form with a large host range, and severely affects Cavendish bananas. Foc TR4 was recently observed within the Greater Mekong Subregion, after Chinese private companies expanded Cavendish production to the region. In this study, extensive surveys conducted across Laos and Vietnam show that Foc TR4 is still mainly constricted to the northern regions of these countries and is limited to Cavendish cultivation settings. In Laos, Foc TR4 is associated with large-scale Cavendish plantations owned by or involved with Chinese companies through which infected planting material could have been imported. In Vietnam, mostly small-holder Cavendish farmers and backyard gardens were affected by Foc TR4. In Vietnam, no direct link is found with Chinese growers, and it is expected the pathogen mainly spreads through local and regional movement of infected planting materials. Foc TR4 was not recorded on banana cultivars other than Cavendish. The extensively cultivated ‘Pisang Awak’ cultivar was solely infected by VCGs belonging to Foc race 1 and 2, with a high occurrence of VCG 0123 across Laos, and of VCG 0124/5 in Vietnam. Substantial diversity of Foc VCGs was recorded (VCGs 0123, 0124/5, 01218 and 01221) from northern to southern regions in both countries, suggesting that Fusarium wilt is well established in the region. Interviews with farmers indicated that the local knowledge of Fusarium wilt epidemiology and options for disease management was limited. Clear communication efforts on disease epidemiology and management with emphasis on biosecurity practices need to be improved in order to prevent further spread of Foc TR4 to mixed variety smallholder settings.

show abstract

“…Sample collections and identifications were undertaken as described earlier. In addition to Foc TR4-specific primer sets, Foc Lineage VI-specific primers 24 were used for the molecular identification of collected strains. Foc Lineage VI 25 includes all the Foc races 1 and 2 isolates found in East and Central Africa 11 .…”

Section: On-farm Disease Developmentmentioning

confidence: 99%

Occurrence and spread of the banana fungus Fusarium oxysporum f. sp. cubense TR4 in Mozambique

et al. 2020

View full text Add to dashboard Cite

Fusarium wilt, caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), poses a major threat to banana production globally. A variant of Foc that originated in Southeast Asia, called tropical race 4 (TR4), was detected on a Cavendish banana export plantation (Metocheria) in northern Mozambique in 2013. Foc TR4 was rapidly disseminated on the farm, and affected approximately half a million plants within 3 years. The fungus was also detected on a second commercial property approximately 200 km away (Lurio farm) a year later, and on a small-grower’s property near Metocheria farm in 2015. Surveys in Mozambique showed that non-Cavendish banana varieties were only affected by Foc race 1 and race 2 strains. The testing of Cavendish banana somaclones in northern Mozambique revealed that GCTCV-119 was most resistant to Foc TR4, but that GCTCV-218 produced better bunches. The occurrence of Foc TR4 in northern Mozambique poses a potential threat to food security on the African continent, where banana is considered a staple food and source of income to millions of people. Cavendish somaclones can be used, in combination with integrated disease management practices, to replace susceptible Cavendish cultivars in southern Africa. The comprehensive testing of African cooking bananas for resistance to Foc TR4 is required, along with the improvement of biosecurity and preparedness of growers on the African continent.

show abstract

The development of a multiplex PCR assay for the detection of Fusarium oxysporum f. sp. cubense lineage VI strains in East and Central Africa

Cited by 19 publications

References 47 publications

Genome Sequence Data Reveal at Least Two Distinct Incursions of the Tropical Race 4 Variant of Fusarium Wilt into South America

Genome Sequence Data Reveal at Least Two Distinct Incursions of the Tropical Race 4 Variant of Fusarium Wilt into South America

Geographical Distribution and Genetic Diversity of the Banana Fusarium Wilt Fungus in Laos and Vietnam

Occurrence and spread of the banana fungus Fusarium oxysporum f. sp. cubense TR4 in Mozambique

Contact Info

Product

Resources

About